3V5E | pdb_00003v5e

Crystal structure of ClpP from Staphylococcus aureus in the active, extended conformation

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
N	d3v5en_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
M	d3v5em_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
L	d3v5el_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
K	d3v5ek_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
J	d3v5ej_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
I	d3v5ei_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
H	d3v5eh_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
G	d3v5eg_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
F	d3v5ef_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
E	d3v5ee_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
D	d3v5ed_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
C	d3v5ec_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
B	d3v5eb_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)
A	d3v5ea_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Clp protease, ClpP subunit	automated matches	(Staphylococcus aureus subsp. aureus NCTC 8325 ) [TaxId: 93061 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
N	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ClpP/crotonase	8068479	3000033	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
N	RRM_1	e3v5eN1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
M	RRM_1	e3v5eM1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
L	RRM_1	e3v5eL1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
K	RRM_1	e3v5eK1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
J	RRM_1	e3v5eJ1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
I	RRM_1	e3v5eI1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
H	RRM_1	e3v5eH1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
G	RRM_1	e3v5eG1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
F	RRM_1	e3v5eF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
E	RRM_1	e3v5eE1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
D	RRM_1	e3v5eD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
C	RRM_1	e3v5eC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
B	RRM_1	e3v5eB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (v294.1)
A	I-set	e3v5eA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: I-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
M	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
L	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
K	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
J	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
I	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
H	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
G	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
F	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
E	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
D	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
C	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
B	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
A	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	ATP-dependent Clp protease proteolytic subunit	peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity ATP-dependent peptidase activity ATP-dependent activity ATPase binding protein binding binding enzyme binding identical protein binding	catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process protein quality control for misfolded or incompletely synthesized proteins macromolecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm endopeptidase Clp complex protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR001907	ATP-dependent Clp protease proteolytic subunit	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR018215	ClpP, Ser active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR033135	ClpP, histidine active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR023562	Clp protease proteolytic subunit /Translocation-enhancing protein TepA	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.